2-133574525-C-T

Variant names:

• chr2-133574525-C-T
• rs891821
• XM_005263660.5:c.-61-56938G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_005263660.5(NCKAP5):​c.-61-56938G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,352 control chromosomes in the GnomAD database, including 19,244 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (19244 hom., cov: 30)
• Consequence: NCKAP5 XM_005263660.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 3 publications found

Genes affected

NCKAP5 (HGNC:29847): (NCK associated protein 5) Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74630 AN: 151238 Hom.: 19230 Cov.: 30

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.450

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.493 AC: 74682 AN: 151352 Hom.: 19244 Cov.: 30 AF XY: 0.499 AC XY: 36864 AN XY: 73868

African (AFR) AF: 0.355 AC: 14610 AN: 41168

American (AMR) AF: 0.453 AC: 6894 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1650 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2407 AN: 5114

South Asian (SAS) AF: 0.579 AC: 2779 AN: 4796

European-Finnish (FIN) AF: 0.651 AC: 6745 AN: 10368

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38079 AN: 67904

Other (OTH) AF: 0.452 AC: 951 AN: 2102

Alfa AF: 0.524 Hom.: 60152

Bravo AF: 0.467

Asia WGS AF: 0.542 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		-0.089

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs891821; hg19: chr2-134332096;